napistu.ingestion.trrust

Functions

`convert_trrust_to_sbml_dfs`(trrust_uri[, ...])	Ingests trrust to sbml dfs
`download_trrust`(target_uri)	Downloads trrust to the target uri

napistu.ingestion.trrust._format_pubmed_for_interactions(pubmed_set): Format a set of pubmed ids as an Identifiers object.

napistu.ingestion.trrust._get_uniprot_2_symbol_mapping(organismal_species: str | OrganismalSpeciesValidator = 'Homo sapiens', preferred_method: str = 'bioconductor', allow_fallback: bool = True) → DataFrame

Create a mapping from Uniprot IDs to gene symbols using Genodexito.

Parameters:

species (str, optional) – The species to create mappings for, by default LATIN_SPECIES_NAMES.HOMO_SAPIENS
preferred_method (str, optional) – Preferred method for identifier mapping, by default GENODEXITO_DEFS.BIOCONDUCTOR
allow_fallback (bool, optional) – Whether to allow fallback to alternative mapping methods, by default True

Returns:

DataFrame with columns for gene symbol and UniProt ID mappings

Return type:

pd.DataFrame

napistu.ingestion.trrust._read_trrust(trrust_uri: str) → DataFrame

Read trrust csv

Parameters:: trrust_uri (str) – uri to the trrust csv
Returns:: Data Frame
Return type:: pd.DataFrame

napistu.ingestion.trrust._summarize_trrust_pairs(pair_data: DataFrame) → Series: Summarize a TF->target relationship based on the sign and source of the interaction.

napistu.ingestion.trrust.convert_trrust_to_sbml_dfs(trrust_uri: str, organismal_species: str | OrganismalSpeciesValidator = 'Homo sapiens', preferred_method: str = 'bioconductor', allow_fallback: bool = True) → SBML_dfs

Ingests trrust to sbml dfs

Parameters:

trrust_uri (str) – trrust uri
organismal_species (str | OrganismalSpeciesValidator) – organismal species
preferred_method (str) – preferred method
allow_fallback (bool) – allow fallback

Returns:

sbml dfs

Return type:

SBML_dfs

napistu.ingestion.trrust.download_trrust(target_uri: str) → None

Downloads trrust to the target uri

Parameters:: target_uri (str) – target url
Return type:: None